CHARMM Development Project Forums User Discussion & Questions Installation and Testing AMD64 bi installation

I have AMD-64bit mechines with ubuntu installed when i configured charmm with

./install.com gnu large AMD64

Fri Jun 22 18:01:21 CEST 2007

install.com> Directory /media/sdb1/charmcheck/c32b1/build/gnu does not exist.
Creating /media/sdb1/charmcheck/c32b1/build/gnu ...

install.com> Phase 1 completed.

install.com> The preprocessor prefx_gnu installed.

install.com> Phase 2 completed.

install.com> Processing CHARMM source on gnu...


install.com> The CHARMM executable
/media/sdb1/charmcheck/c32b1/exec/gnu/charmm is NOT produced.
Check /media/sdb1/charmcheck/c32b1/build/gnu/gnu.log
for installation errors.

install.com> Phase 3 completed.


and the error in gnu.log file has


Conditional keys: REPLICA RGYCONS RXNCOR SASAE SCPISM SGLD SHAPES SHELL SOFTVDW TNPACK TPS TRAVEL
Conditional keys: TSM TSALLIS FITCHG SLVSLV LNTAB1 WCA QUANTUM NOGRAPHICS
g77 -mcmodel=medium -ffast-math -funroll-loops -march=k8 -fno-globals -Wno-globals -c -O2 univio.f
ar rucv /media/sdb1/charmcheck/c32b1/lib/gnu/io.a univio.o
a - univio.o
/bin/rm -f univio.f
/bin/rm -f univio.o
ranlib /media/sdb1/charmcheck/c32b1/lib/gnu/io.a
io COMPLETED
gcc -Dnographics -O -Dgnu -DLINUX -c /media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c
/media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c: In function ‘fmalloc_’:
/media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c:104: warning: conflicting types for built-in function ‘malloc’
/media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c: In function ‘fsystem_’:
/media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c:145: warning: incompatible implicit declaration of built-in function ‘exit’
/media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c: In function ‘gethdir_’:
/media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c:177: warning: incompatible implicit declaration of built-in function ‘strncpy’
/media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c:183: warning: incompatible implicit declaration of built-in function ‘strlen’
/media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c:188: warning: incompatible implicit declaration of built-in function ‘strcpy’
/media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c:188: warning: incompatible implicit declaration of built-in function ‘strlen’
/media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c: In function ‘fgetenv_’:
/media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c:232: warning: incompatible implicit declaration of built-in function ‘strcpy’
/media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c:233: warning: incompatible implicit declaration of built-in function ‘strlen’
/media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c: In function ‘fputenv_’:
/media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c:272: warning: incompatible implicit declaration of built-in function ‘strcpy’
/media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c:278: warning: incompatible implicit declaration of built-in function ‘exit’
/media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c: In function ‘filcpy_’:
/media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c:317: warning: incompatible implicit declaration of built-in function ‘strncpy’
/media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c: In function ‘getunamef_’:
/media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c:375: warning: incompatible implicit declaration of built-in function ‘strlen’
/media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c:380: warning: incompatible implicit declaration of built-in function ‘strncpy’
/media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c: In function ‘etime_’:
/media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c:408: error: ‘CLK_TCK’ undeclared (first use in this function)
/media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c:408: error: (Each undeclared identifier is reported only once
/media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c:408: error: for each function it appears in.)
/media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c: In function ‘loc_’:
/media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c:622: warning: cast from pointer to integer of different size
/media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c: In function ‘fdate_’:
/media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c:682: warning: incompatible implicit declaration of built-in function ‘strncpy’
/media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c: In function ‘uninf_’:
/media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c:948: warning: incompatible implicit declaration of built-in function ‘strlen’
/media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c:950: warning: incompatible implicit declaration of built-in function ‘strncpy’
/media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c: In function ‘binarytesthdrr_’:
/media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c:1139: warning: incompatible implicit declaration of built-in function ‘strncpy’
/media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c:1141: warning: incompatible implicit declaration of built-in function ‘strlen’
make: *** [/media/sdb1/charmcheck/c32b1/lib/gnu/machdep.a(cstuff.o)] Error 1

should i need to use 32bit libraries inorder to solve it. could you please advice me the alternative ideas to install in amd64 bit mechines and how could i use the command.

thanks in advance

At the very least, you probably need to make sure that gcc and g77 are from the same release version of the GCC suite; try the --version flag for the compilers.

I have following compilers in my mechine


gcc --version
gcc (GCC) 4.1.1 20070105 (Red Hat 4.1.1-52)
Copyright (C) 2006 Free Software Foundation, Inc.
This is free software;

g77 --version
GNU Fortran (GCC) 3.4.6 20060404 (Red Hat 3.4.6-4)
Copyright (C) 2006 Free Software Foundation, Inc.

The gcc version mismatch could be a problem; I've not used g77 for CHARMM on 64-bit machines, so I'm not sure how to advise you further.

g77 comes from the compatibility package compat-gcc-34-g77. You should install the corresponding gcc compatibility package which is called compat-gcc-34 and modify Makefile.gnu to use gcc34 instead of gcc. However, this combination is quite likely to produce a CHARMM executable which would not be fully functional, f.e. the large memory allocations might fail.

The other possibility is to modify the same Makefile.gnu and change g77 into gfortran, while leaving gcc as is. This is more likely to produce a well behaving executable than g77+gcc34.

intel compiler works fine for 64bit mechines


./install.com gnu large ifort AMD64